[gmx-users] quick clarification on free energy and domain decomposition

[Michael Shirts]

Hi, all-

I wanted to check quickly.  I noticed a difference in domain
decomposition when I ran with free energy on and off (using the
coupl-mol functionality), with a relatively large molecule (8 residue
peptide) being decoupled.  Domain decomposition failed for the free
energy on 4 cores, and looking at the log file I noticed:

No free energy:
<     two-body bonded interactions: 0.434 nm, LJ-14, atoms 340 348

---
Free energy:
>     two-body bonded interactions: 2.586 nm, LJC Pairs NB, atoms 1727 1809

I'm sure people have noticed this before, but I'm wondering if there
is some workaround?  If I mutate the atoms directly rather than using
coupl-mol, would I be able to get around it?

Thanks!